When considering DNA isolation from formaldehyde-fixed chromatin for ChIP-qPCR, the PCI method and the Chelax 100 method present distinct advantages and disadvantages. The PCI method, involving phenol-chloroform-isoamyl alcohol, is widely employed due to its efficacy in removing proteins and lipids, ensuring purity across various sample types. However, it requires careful handling of toxic phenol and requires multiple centrifugation steps, with the risk of DNA degradation if not executed meticulously. On the other hand, the Chelax 100 method offers simplicity and speed, bypassing the need for hazardous phenol, making it suitable for smaller-scale extractions. Nevertheless, it may not be as thorough in removing proteins and lipids as the PCI method, and its less prevalent in ChIP assays may necessitate validation for reliability. Overall, while the PCI method is generally preferred for its robustness, the Chelax 100 method could serve as a viable alternative, particularly when validated and suitable for specific experimental requirements.

References:

Khan SS, Tijare M, Kasetty S, Jain M, Alamoudi A, Bahammam HA, Bahammam SA, Bahammam MA, Varadarajan S, Raj AT, et al. Evaluation and Comparison of Genomic DNA Extraction Methods and PCR Optimization on Archival Formalin-Fixed and Paraffin-Embedded Tissues of Oral Squamous Cell Carcinoma. Diagnostics. 2022; 12(5):1219. https://doi.org/10.3390/diagnostics12051219